Resources
Description of resource files and executables
There are various resource files and executables needed for this pipeline. If you are working on JUNO, you should be fine as default options will work fine for you. For other users, here are a list of resources needed in various steps in the pipeline, and their descriptions
Pooled bam directory
Directory containing list of donor bams (unfiltered) to be genotyped for systematic artifact filtering
Default:
/work/access/production/resources/msk-access/current/novaseq_curated_duplex_bams_dmp/current/
Fasta
Hg19 human reference fasta
Default:
/work/access/production/resources/reference/current/Homo_sapiens_assembly19.fasta
Genotyper
Path to the GBCMS genotyper executable
Default:
/ifs/work/bergerm1/Innovation/software/maysun/GetBaseCountsMultiSample/GetBaseCountsMultiSample
DMP IMPACT Github Repository
Repository of DMP IMPACT data updated daily through the cbio enterprise github
Default:
/juno/work/access/production/resources/cbioportal/current/mskimpact
DMP IMPACT raw data
Mirror bam directory
Directory containing list of DMP IMPACT bams
Default:
/juno/res/dmpcollab/dmpshare/share/irb12_245/
Mirror bam key file -- ONLY 'IM' (SOLID TISSUE) SAMPLES ARE GENOTYPED
File containing DMP ID - BAM ID mapping
Default:
/juno/res/dmpcollab/dmprequest/12-245/key.txt
Need to talk to Aijaz Syed about 12-245 access
>
CH list
list of signed out CH calls from DMP
Default:
/juno/work/access/production/resources/dmp_signedout_CH/current/signedout_CH.txt
DMP IMPACT Github Repository
Repository of DMP IMPACT data updated daily through the cbio enterprise github
Default:
/juno/work/access/production/resources/cbioportal/current/mskimpact
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